


Penitence

by Oreo_Believer



Category: Marvel Cinematic Universe, Spider-Man - All Media Types
Genre: BAMF Michelle Jones, Bisexual Peter Parker, Bully Flash Thompson, Captain America: Civil War (Movie) Compliant, Flash Thompson Being A Jerk, Gen, Good Friend Ned Leeds, How Do I Tag, Intern Peter Parker, Irregular Upload Schedule, Jonah Brooks is a Good Bro, Michelle Jones Is a Good Bro, Ned Leeds is a Good Bro, Original Character Jonah Brooks, Other Additional Tags to Be Added, Post-Spider-Man: Homecoming, Pre-Avengers: Infinity War Part 1 (Movie), Precious Peter Parker, Spider-Man: Homecoming Compliant, Tony Stark Has A Heart, Tony Stark Is a Good Bro, Tony Stark is a sarcastic shit, decathlon team - Freeform, idk if it will come up but always bi peter parker, they all are really
Language: English
Status: In-Progress
Published: 2020-10-05
Updated: 2020-10-05
Packaged: 2021-03-07 22:08:08
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 3,395
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/26824891
Author URL: https://archiveofourown.org/users/Oreo_Believer/pseuds/Oreo_Believer
Summary: After the homecoming fiasco, things are going smoothly for Peter. He's started a legitimate internship under Tony Stark, and after MJ took over as captain of the decathlon team and forced Peter to spend more time with the team, he actually feels like a normal teenage boy. Everything is smooth sailing, the world keeps turning. Then, on a seemingly normal winters day, a new boy walks into school...(Takes place after SpiderMan: Homecoming)
Relationships: Ned Leeds & Original Character(s), Ned Leeds & Peter Parker, Peter Parker & Michelle Jones, Peter Parker & Original Character, Peter Parker & Tony Stark
Comments: 1
Kudos: 25





	Penitence

It had been a normal few months at Midtown High School. After the fiasco during homecoming, things had really settled down for the school. With the loss of Liz to Oregon, a lot of the senior class, as well as the decathlon team, felt the lack of her presence. However, the world continues to spin, and like all things, the event was quickly forgotten in favor of new things. 

When Liz moved, Michelle Jones, better known as MJ, took over as captain of the decathlon team. Nobody protested, including the older kids on the team. They all knew MJ deserved this most, considering she was the smartest of all of them. MJ accepted the position, and practice started up again. 

She had also started forcing one Peter Parker to start attending more practices. By now, she knew exactly what the Stark Internship entailed, but she didn’t care. As important as saving all of Queens was, she made sure he also participated in normal teenage things. 

Peter really didn’t mind. He actually thought it was nice to be able to take some time and enjoy the decathlon practices. Between that, school, and an actual internship at Stark Industries working under Tony Stark himself, he was pretty busy. Tony and May (after the initial shock of finding out her nephew was a crime-fighting vigilante after school) even helped him come up with a schedule for patrolling so he didn’t get too overwhelmed. 

So yeah, Peter would say that things have gotten increasingly better since he crashed a plane into a lake and his maybe-girlfriend moved away after he took down her dad. 

As he walked into school on a surprisingly sunny December day, he was greeted by his best friend, Ned Leeds. Ned and Peter had always been close, but they’d definitely gotten a lot closer since Ned became his Guy-in-the-Chair. Ned waved him over to his locker, a big smile on his face. Peter smiled and rolled his eyes, walking over to him. Ned’s smile was contagious against everybody, even MJ occasionally couldn’t resist smiling back at him. 

“What’s up, Ned?” Peter asked, opening his locker to fish out his English textbook. English was his least favorite subject, so he kept the book in his locker at night to avoid doing work, much to the dismay of his teacher.

“Dude, you’ll never believe it! MJ kicked Flash off of the decathlon team!” 

Peter almost dropped his textbook on his foot, jumping out of the way just in time. His mouth fell open in surprise, and he knew that if MJ were here, she’d be mentally taking a picture of him to sketch later. 

“Are you serious? That’s...wow! That’s amazing!” Ned nodded excitedly, which made Peter chuckle a bit. “So...wait, who’s going to replace him? We need the extra person on our team.”

Flash had been the alternate on the team for a while, usually covering for Peter before he became more present and Liz left. Once Liz left, and MJ moved up to captain, the standings of the entire team shifted, making Flash a permanent member of the team, until now. 

“I don’t know man, MJ just told me something a few minutes ago about finding a replacement for him after school tomorrow,” Ned responded, shutting Peter’s locker for him as Peter bent down to put his book in his backpack. 

“Speaking of which, you both are required at practice tomorrow,” MJ said, seemingly appearing out of nowhere, making both of the boys jump. Peter never understood how she did that. He had a sixth sense to tell him when someone was approaching, even if he couldn’t see them, and somehow MJ always managed to scare him. Thank god she wasn’t a bad guy, he thought, and then amended the thought as there was a lot he didn’t know about her and she very well could be a bad guy. 

Peter nodded. “I think I’ll be at the tower this weekend but I can have Happy pick me up later.” 

“Good. Anyways, I’ve got to go talk to Harrington. He should probably hear it from me that Flash was kicked. Unless that dumbass already went to tattle on me. See you later, losers.” With that, MJ turned around and walked the other way. 

Peter’s eyes widened at that, and when he turned to look at Ned, he saw his friend’s face mimicking his.

“I can’t believe she kicked Flash without telling Harrington first,” Ned said, voice barely above a whisper. 

Peter just shook his head. “I guess that’s MJ,” he said. “Come on, we’re gonna be late for English.”

The two hurried down the hall, and they slipped into class just in time. Normally their English teacher, Ms. Phillips, would tell them off, but it seemed she was preoccupied talking to a student Peter didn’t recognize. He decided to just count it as a win and sit down before she was done with the conversation, and Ned followed his lead. 

Ms. Phillips had the student stand in front of the room and began talking. Peter quickly tuned her out, instead focusing his attention on the new boy. He was probably a few inches shorter than Peter was, and he was hunched over slightly, probably nervous to be shown off in front of the whole class like this. He had thick, curly black hair and blue eyes.

When the new boy looked over at Peter, Peter offered him a quick smile, which the boy returned. 

“Why don’t you introduce yourself and tell us a little about yourself?” he heard Ms. Phillips say, and he focused his attention back on the boy, who looked a little less nervous now. 

“Uh, ok. My name is Jonah Brooks. My parents got transferred to New York from St. Louis, Missouri. I have a little brother and a cat.” Jonah turned back to the teacher. “I think that’s enough?” 

Ms. Phillips nodded. “You can take a seat, Jonah. There should be a free one in the third row.” Peter smiled as Jonah took a seat right in front of Ned, and smiled back at him. 

After that, English went by pretty fast, probably because Peter completely ignored what they were learning, opting instead to scroll through his phone under his desk. Before long, the bell rang, and Peter, Ned, and Jonah all stood up to leave. 

Ned stuck his hand out to Jonah eagerly. He may be just as awkward as Peter was, but he didn’t have the social anxiety Peter did, so he absolutely loved meeting new people. “Hi! My name is Ned, and this is my best friend Peter. We also have another friend named MJ; well, her real name is Michelle but she lets us call her MJ, but she has a different first hour so she’s not here. You can meet her at lunch! If you want to eat with us, that is.”

Peter mentally facepalmed at his friend’s rambling, worried Ned was going to scare Jonah away, but the new boy just smiled. 

“That sounds nice,” he said, shaking Ned’s hand. “I haven’t really met that many people in New York yet. You guys seem nice.” 

Peter smiled as well, relieved with how well that went. “Well, we’d love to have you at lunch. What’s your next hour, maybe we could show you there?” 

Jonah smiled, taking out his schedule. “I have Chemistry with a… Mr. Harrington?” 

Ned’s eyes lit up at that, and Peter couldn’t hold back a chuckle at the sight. His best friend’s face was always so animated, the opposite of MJ’s. 

“We have Harrington next too! This is perfect! Hopefully, he’ll let us work together in the lab! Usually, there’s only supposed to be two people together but since the class is already partnered up he’ll probably make an exception. Come on, let’s go!” 

Peter once again expected Jonah to get intimidated or annoyed with Ned’s rambling, but Jonah just smiled at him and nodded. “Lead the way.” 

Their walk was uneventful, but when they approached the room, Peter could hear yelling. His super-hearing made the voices loud and clear before the other two could even hear anything. 

“You can’t just kick me from the team for no good reason!” Peter grimaced. This was about how he expected it to go.

“I can do whatever the fuck I want, I’m the captain.” And, this seemed about right for MJ, as well. 

“Michelle!” Harrington sounded exhausted. This had probably been going on for a while, maybe the whole first period. 

“Wait til I tell my father about this, dumbass! He’ll make you wish you were never born!”

“Flash!” 

“Well you can tell your father he can take his comments and he can shove them up his-”

“Both of you! Stop!”

Peter turned the handle to Harrington’s classroom and was met with quite a sight. Flash was standing off to one side of the room, his face as red as a fire engine. He appeared to be absolutely fuming. On the other side of the room stood MJ, looking...well, MJ. Her face didn’t have any emotion, and she was looking down at her nails on one hand, seemingly disinterested by the other’s shouting. And in the middle was Roger Harrington himself. Peter couldn’t help but feel bad for the man. He looked exhausted, sick of their fighting. 

“Flash, Michelle has brought up some good points. You’ve been a bad sport, and rude to the other team members. I think it’s appropriate that you are off the starting team, but you may stay on as an alternate in a probationary period. I better not hear of any more bad behavior from you. ”

Flash seemed satisfied at that, the red of his face disappearing and his mouth melting back to his usual smirk. He went to sit in the back row where some of his friends were already waiting. 

Peter didn’t mind him being an alternate again any more than he’d minded it last time. Flash will still be around, and obnoxious, but at least he’ll be back to sitting on the bench during competitions. 

“Michelle, I would appreciate it if you’d give me a heads up in the future if you’re deciding to kick a member of the team off of the roster.”

MJ shrugged, gave him a look that said “no promises”, and promptly walked out of the room. 

“That’s MJ?” Peter heard Jonah whisper, which made him laugh. He nodded, to which Jonah just replied with a quiet, “Badass.” 

—————————

MJ was already waiting at their usual table when Peter and company approached, reading Pride and Prejudice for the umpteenth time. When she saw them approaching, she lowered the book a little, raising an eyebrow. 

“Who’s the new kid?” she asked, blunt as ever. At one point, Peter would have shrunk in on himself at the sight of that look. Maybe it was just his anxiety, but man, whenever she did that earlier this year it made him feel like she was staring through him, analyzing him like some sort of science project. Now, it only made him smile. He wondered when that change happened but pushed the thought to the back of his mind. 

“This is Jonah,” he said, waving a hand in front of the new boy. “He just moved here from Missouri. We invited him to sit with us since he doesn’t know anybody.”

If MJ cared, she didn’t show it. Peter studied her, looking for a reaction, but all she did was raise the book back up above her eyes, continuing her reading. “Welcome to the table, loser.”

“She means that in a good way, probably,” he heard Ned whisper to Jonah, making him smile again. “Come on, let’s go get our food. They make popcorn chicken on Thursday’s and it’s the only meal even they can’t mess up.”

The three of them made their way to the lunch line but were stopped short by none other than Flash and his friends. 

“Hey Penis, who’s your new boyfriend? Another friend from the orphanage?”

“Leave them alone, Flash. Just let us go get lunch.” Peter shot Ned a grateful look. He’s always way calmer around Flash.

“Who the fuck do you think you’re talking to, Fatso?”

Peter opened his mouth to respond, fire lighting in his eyes, when he heard Jonah beat him to it. At one glance, the new kid seemed just as mad as he was. 

“Excuse you? Who the fuck are you?”

Flash falters, but quickly gets that same punchable smug look on his face. Oh, what Peter wouldn’t give to punch that face.

“My name is Flash. I’m a big deal around here. My parents are on the school board and they fund most of the school, including the scholarships for poor people like Penis and Fatso, for whatever reason. You should come and hang with us, I can show you around the place and tell you who to stay away from.”

A flash of anxiety ripped through Peter. They hadn’t known Jonah very long, and he figured the new kid would jump at the offer to go hang out with someone like Flash. He chanced a look at Jonah and immediately regretted doubting him. Jonah was staring Flash down, giving him a cocky look that could rival one Tony Stark. He couldn’t help but grin at the similarities. 

“Actually, Flash, I think I’m smart enough to figure out who I should stay away from, starting with you. Come on, Peter, Ned, let’s leave this arrogant prick while he’s still gaping like a fish.” 

He felt Jonah grab onto his arm and pull him away, and he couldn’t help but laugh at the face his bully was making. Maybe he didn’t need to worry about Jonah after all. 

—————————

When Peter got to the Tower and stepped into the elevator after school, he was still wearing a huge smile. After the scene at lunch, he didn’t have any more classes with Jonah or Ned, which sucked, but Ned added Jonah to the group chat, and he’d talked to the two (and occasionally MJ when she popped in to tell them to shut up and go to class) throughout his last two periods. Between that and the excitement of getting to work in the lab after school, it had been a pretty great day. 

Lab days were still fairly new to Peter, but since they started, he’s looked forward to them every day. Since he took down Adrian Toomes and declined the invite to join the Avengers, he and Mr. Stark had gotten a lot closer, much to Peter’s relief. When he declined the offer to join the team of superheroes (or what’s left of it, anyway), he worried that it meant his connection with Tony had ended as well. However, Tony offered him an actual internship at SI, working directly under him and helping him out in the lab every Tuesday and Thursday after school, as well as every other weekend. 

(Peter often referred to that arrangement as “Split Custody”, much to Tony’s horror. The only reason he kept doing it was because he loved the face his mentor made when he casually slipped the phrase into conversations. He’d recently gotten May to join in on the joke, to which Tony only replied with feigned hurt and “I can’t believe both of you would gang up on me like this.”)

Peter pulled himself out of his musings when the elevator doors opened and FRIDAY alerted him that he had reached his destination. Peter thanked her as he shuffled out. 

“Hey, Pete! Glad you’re here! I need a little help with something!” Peter raised an eyebrow quizzically. His mentor’s voice sounded far away. 

“Where are you?”

“Back here! I had a bit of a… situation... with Dum-E. He’s constantly living up to his name.”

He heard what sounded like angry chirping coming from the back of the lab, and he chuckled, making his way over to Stark. 

“I agree, Dum-E. Strong words from a man who owes you his life,” Peter teased.

“I regret telling you that story, kid. Anyways. There may have been a tiny explosion back here earlier. Not important how it happened. Dum-E decided to try and put out the little fire, but he drove through it and spread it around the lab, and then assaulted me with his fire extinguisher.”

When Peter turned the corner to the scene of the crime, he couldn’t help but break out into laughter. A small corner of the lab and a lot of the outer metal on Dum-E had turned black and brown from the fire. Tony Stark was standing a couple of feet away with a small toolbox, fully covered in white foam, looking completely and totally done.

“Thanks, kid, that’s very helpful,” he deadpanned.

“I’m sorry, Mr. Stark, but this is hilarious.” 

Tony rolled his eyes, but there was no heat behind it. “Great. My own robot and my own intern, turning their back on me in my darkest hour. What did I do to deserve this?”

“Oh, don’t be so dramatic Mr. Stark,” Peter playfully chastised. Dum-E seemed to get the memo and chirped at him with the same level of attitude. Peter grabbed his phone out and snapped a picture before his mentor could stop him. “I’m definitely sending this to Ms. Potts.”

“I regret the day I ever let you two meet. That was a terrible decision and I am paying for it greatly.” 

Peter put his phone away after sending off the picture, and he grabbed a towel off of a nearby stool. He tossed it to Tony, who grabbed it and started wiping his skin off. 

“I wish I could say this is the first time this has happened.”

Peter laughed at that, setting down his backpack. He dug out an English worksheet that was crumpled up at the bottom of his bag. The date at the top indicated that this assignment was due over two weeks ago. 

Part of May’s conditions for taking the internship and continuing to patrol was that Peter needed to keep his grades up. He didn’t have a problem with science and math classes, but he absolutely hated English.

“Great organizational skills there, kid,” he heard Tony say, voice thick with sarcasm. 

“Says you,” Peter snorted, starting on the assignment. It was just a long list of ACT/SAT vocabulary words they’d started learning earlier that year. 

“Whatever. Do your work, Spiderboy. I’m gonna shower quick, and I want to work when I come back.”

Once Peter got to work, he’d actually flown through the assignment. Not that he’d ever admit that, lest they start making him do his English homework more often. Just as he was finishing it up, his mentor walked back in, wearing a different pair of sweatpants and a new sweatshirt. 

“You finished, kid?” When Peter nodded, he continued. “Why don’t you come and help me with Dum-E, replacing his roasted parts and all that jazz.”

Peter laughed, shoving his paper back into the depths of his backpack, probably never to be seen again. He sauntered over to where the bot was sitting, immediately getting to work.

“So, kid, how was your day?”

“Not as interesting as yours,” the boy jabbed. Tony rolled his eyes, making Peter laugh. 

“It was pretty good, though. I met a new kid, and Flash got sent back to being an alternate on the decathlon team. Plus I aced my Spanish quiz, I mean I studied really hard for it but I wasn’t sure if I would actually do that well on it, so that was a nice surprise.”

His mentor chuckled. “I’m glad it was a good day.” 

The two fell into a comfortable silence, slowly fixing Dum-E, while the bot in question chirped playfully, seemingly loving the attention. When they finished, Peter checked the time.

“Wow, it’s almost time for me to be home! I better go, I have some homework to get done still!”

“Alright, kid. You’re staying for the weekend, though, right?” 

“Yes,” he said, quickly gathering his things. “Can you tell Happy to pick me up later, though? MJ says we all have to go to practice tomorrow. She’s holding tryouts for Flash’s spot.” 

“Sure thing, kiddo. I’ll see you then.”

Peter waved, sprinting out the door, already excited for tomorrow.

**Author's Note:**

> Well, there's the first chapter! I hope everyone enjoys it, feel free to tell me what you think if you want, or just leave a kudos if you enjoy the story. It only took me a few days to write but I'm not sure when I'll have the second chapter up because pandemic means crazy school schedule... I'm hoping to have the second chapter done by next week though.
> 
> Thank you to zinc_err for the beta read! If you want, you can find me on tumblr (truthbetheoreos) and make requests and stuff. 
> 
> Anyways, thanks for the read, see ya soon!


End file.
